Collect information about the package annotation DB

Description

Some convenience functions for getting a connection object to (or collecting information about) the package annotation DB.

Usage

  lumiHumanIDMapping_dbconn()
  lumiHumanIDMapping_dbfile()
  lumiHumanIDMapping_dbInfo()

Details

lumiHumanIDMapping_dbconn returns a connection object to the package annotation DB. IMPORTANT: Don't call dbDisconnect on the connection object returned by lumiHumanIDMapping_dbconn or you will break all the AnnDbObj objects defined in this package!

lumiHumanIDMapping_dbfile returns the path (character string) to the package annotation DB (this is an SQLite file).

lumiHumanIDMapping_dbInfo prints other information about the package annotation DB.

Value

lumiHumanIDMapping_dbconn: a DBIConnection object representing an open connection to the package annotation DB.

lumiHumanIDMapping_dbfile: a character string with the path to the package annotation DB.

lumiHumanIDMapping_dbInfo: none (invisible NULL).

See Also

dbConnect

Examples

  ## Show the database information (meta data)
  lumiHumanIDMapping_dbInfo()  

  ## List the tables included in the database
  library(DBI)
  conn <- lumiHumanIDMapping_dbconn()
  dbListTables(conn)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(lumiHumanIDMapping)
Loading required package: lumi
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/lumiHumanIDMapping/lumiHumanIDMapping_dbconn.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lumiHumanIDMapping_dbconn
> ### Title: Collect information about the package annotation DB
> ### Aliases: lumiHumanIDMapping_dbconn lumiHumanIDMapping_dbfile
> ###   lumiHumanIDMapping_dbInfo
> ### Keywords: utilities datasets
> 
> ### ** Examples
> 
>   ## Show the database information (meta data)
>   lumiHumanIDMapping_dbInfo()  
            name        value
1 REFSEQ VERSION             
2       ORGANISM Homo sapiens
3        SPECIES        Human
4   MANUFACTURER     Illumina
> 
>   ## List the tables included in the database
>   library(DBI)
>   conn <- lumiHumanIDMapping_dbconn()
>   dbListTables(conn)
 [1] "HUMANREF8_V3_0_R1_11282963_A_WGDASL" "HumanHT12_V3_0_R3_11283641_A"       
 [3] "HumanHT12_V4_0_R1_15002873_B"        "HumanHT12_V4_0_R2_15002873_B"       
 [5] "HumanHT12_V4_0_R2_15002873_B_WGDASL" "HumanRef8_V1"                       
 [7] "HumanRef8_V2_0_R2_11223162_A"        "HumanRef8_V2_0_R4_11223162_A"       
 [9] "HumanRef8_V3_0_R0_11282963_A"        "HumanRef8_V3_0_R3_11282963_A"       
[11] "HumanWG6_V1"                         "HumanWG6_V2_0_R2_11223189_A"        
[13] "HumanWG6_V2_0_R4_11223189_A"         "HumanWG6_V2_11223189_B"             
[15] "HumanWG6_V3_0_R3_11282955_A"         "metadata"                           
[17] "nuID_MappingInfo"                   
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>